1 Answer
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Without seeing how you've customized the plugin, I can only go off the code of the stock plugin. By default, it will either use the permalink or whatever you have set in the post meta for simple_nivo_link. Here's the actual code:

In English, this code loops through every post in your slider. It calls the_post() to populate the regular template tag functions you know and love. Then it checks to see if you're manually settings the link for the slide by putting something in the simple_nivo_link custom field for the post. If you are, it uses that. If you aren't, it uses the permalink.

However, if you have "none" set in this post meta field, the slider will omit the link entirely.

So, by default, the plugin will do exactly what you expect it to do. If it's not outputting the permalink, then you've changed something in the code that you need to un-change.

Thanks for this response, I've only customized the CSS and have not touched the related code. In fact I just double checked the code you pasted and I have exactly that in tact, and still only the first slide links normally? Any suggestions?
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YourConsciousApr 27 '12 at 14:55

How exactly are the other slides linking? Are they not outputting a link at all? Is the simple_nivo_link custom field populated with any data? From what you've told us so far, this should be working fine ... so there's something about your setup that's preventing it from functioning normally. If there is no link whatsoever, that means somehow that simple_nivo_link is being set to "none" for your other slides ...
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EAMann♦Apr 27 '12 at 15:14